Maize Epigenomic Variation

PI: Nathan M.施普林格（明尼苏达大学-双城分校）CoPI: Matthew W. Vaughn（冷泉港实验室）合作者：Irina Makarevitch（哈姆林大学）人们对理解表观遗传变异如何导致表型变异越来越感兴趣。表观遗传变异，即不因序列变化而产生的可遗传变异，在许多生物现象中已被观察到。然而，表观遗传变异的流行和遗传行为尚不清楚。本项目将研究玉米表观遗传变异的流行、遗传力和潜在后果。将对玉米自交系B73的几个组织和一组26个自交系进行DNA甲基化、组蛋白H3赖氨酸9二甲基化和组蛋白H3赖氨酸27三甲基化的全基因组分析，这些自交系捕获了玉米的大部分多样性。通过关注这一群体，有可能将表观基因组数据添加到丰富的现有遗传和表型信息数据中。这将为识别导致物种表型变异的表观遗传变异的例子提供潜力。该项目还将研究杂交和重组自交系的表观遗传差异是如何遗传的，以评估多代表观遗传变异的稳定性，这对于理解表观遗传变异的遗传性及其与可遗传表型变异的关系至关重要。此外，我们对表观遗传学在自然变异中的作用所知相对较少。为了更详细地了解表观遗传学的作用，了解这种行为是如何遗传的以及这种变异是如何在一个物种内产生的至关重要。该项目将开发用于玉米表观基因组研究的工具，并将为考虑玉米自交系表观遗传变异的频率和稳定性提供框架，并可能为将遗传和表观遗传变异整合到植物育种和改良项目中提供框架。该研究项目将为处于职业生涯不同阶段的科学家提供一系列优秀的培训机会。明尼苏达大学和哈姆林大学的本科生将参与初步研究，并将接受博士后科学家和主要研究人员的指导。博士后科学家和一名研究生将进行基于假设的研究，为基因组学和生物信息学提供经验。此外，两位主要研究人员都表明了对普遍推广的承诺。拓展工作将包括公共教育和K-12教师培训。该项目产生的所有数据将通过GEO （www.ncbi.nlm.nih.gov/geo/）、Gramene （www.gramene.org）和MaizeGDB （www.maizegdb.org）等已建立的数据库以及项目网站公开提供。拟议中的项目还将对其他研究产生更广泛的影响。在这个项目中获得的信息将影响育种和进化的研究。对物种内变异来源的更深入了解将影响许多领域的观点。

PI: Nathan M. Springer (University of Minnesota - Twin Cities)CoPI: Matthew W. Vaughn (Cold Spring Harbor Laboratory)Collaborator: Irina Makarevitch (Hamline University)There is a growing interest in understanding how epigenetic variation might contribute to phenotypic variation. Epigenetic variation, heritable variation that is not due to sequence changes, has been observed in a number of biological phenomena. However, the prevalence and heritable behavior of epigenetic variation is not well understood. This project will study the prevalence, heritability and potential consequences of epigenetic variation in maize. Whole genome profiling of DNA methylation, histone H3 lysine 9 dimethylation and histone H3 lysine 27 trimethylation will be performed on several tissues of the maize inbred line B73 and on a set of 26 inbred lines that capture much of the diversity of maize. By focusing on this population it is possible to add epigenomic data to a wealth of existing data on genetic and phenotypic information. This will provide the potential to identify examples of epigenetic variation that contribute to phenotypic variation within a species. The project will also study how epigenetic differences are inherited in hybrids and recombinant inbred lines to assess the stability of epigenetic variation over multiple generations, which is critical to understanding the heritability of epigenetic variation and how it might be relevant to heritable phenotypic variation. In addition, relatively little is known about the role of epigenetics in natural variation. In order to provide a more detailed understanding of the role of epigenetics, it is critical to understand how this behavior is inherited and how this variation arises within a species. This project will develop tools that will enable epigenomic research in maize and will provide a framework for considering the frequency and stability of epigenetic variation among maize inbred lines and may provide a framework for integrating both genetic and epigenetic variation into plant breeding and improvement projects.The research project will provide a set of excellent training opportunities for scientists at various stages of their careers. Undergraduate students from the University of Minnesota and Hamline University will be involved with the primary research and will receive mentoring from post-doctoral scientists and principal investigators. Postdoctoral scientists and a graduate student will perform hypothesis-based research that will provide experience with genomics and bioinformatics. In addition, the principal investigators have both shown a commitment to general outreach. Outreach efforts will include public education and K-12 teacher training. All data produced by this project will be made publicly available through established databases such as GEO (www.ncbi.nlm.nih.gov/geo/), Gramene (www.gramene.org) and MaizeGDB (www.maizegdb.org) as well as through a project website. The proposed project will also have broader impacts on other research. The information obtained in this project will influence studies of breeding and evolution. A greater understanding of the sources of variation within a species will influence the view of many fields.